Ruben Abagyan

Academic Achievements

Education: S.c. laude M.S. in Molecular and Chemical Biophysics (1980) Moscow Inst. Physics & Technology; Ph.D. in Protein Structure Prediction (1984) Moscow State University.

Academic Position:

  • Liege Belgium (visiting scientist),
  • EMBL Heidelberg (staff scientist),
  • New York University, NYU Medical School, The Courant Institute of Mathematics (tenured associate professor of biochemistry and mathematics),
  • The Scripps Research Institute in La Jolla (professor),
  • University of California, San Diego (professor)

Awards and Honors:

  • Two CapCure awards for excellence in prostate cancer research (2000, 2002).
  • Princess Diana Award and Medal, Sydney (2003).
  • UCSD Faculty and Staff Excellence Award (2007).
  • AACP’s 2016 Teacher of the Year Award
  • SSPPS Student-voted Faculty of the Year Award (2018). H-index: 100
  • Recognition as top 1% most performing and cited faculty, (2018).

Leadership Experience:

  • Director of Computational Biology & IT at Skirball Inst. of Biomolecular Medicine, New York (1994-1999);
  • Director at Novartis Institute, GNF (1999-2002);
  • Structure-Based Drug Discovery Chair, MipTec, Basel, Switzerland (2002-2009);
  • Founder of MolSoft (1994);
  • Member of the Board of Directors of Syrrx (2001-2002);
  • SAB Member of Plexus Vaccines (2001- 2003);
  • Editorial Boards (current):
    • Endocrine Disruptors,
    • Am.J.Pharm.Tox
    • Cancer Genomics and proteomics,
    • IUPAC Glossary Committee,
    • J.Comp- Aided Mol.Des.
    • Steering Committee member of UCSD Bioinformatics and Systems Biology Graduate Program,
    • the Swiss NSF NCCR- Transcure Center, and Hong Kong State Key Laboratory of Chemical Biology;
    • Review Panel member at the European Research Council Synergy Program, Brussels (2018,2019,2022, 2023,2024)


  • Pharmaceutical Chemistry II, Physical Pharmacology (SPPS 222)
  • Principles of Pharmaceutical Sciences and Drug Development (SPPS 263A)
  • Bioinformatics and Systems Biology research seminar co-director (BNF 199)

Key Contributions

  • Internal Coordinate Mechanics (ICM), formulation, algorithms, and code, for structure sampling, dynamics, molecular docking, peptide and protein docking, drug candidate screening.
  • Stochastic global conformational sampling and global energy minimum search for multi-molecular ensembles in internal coordinates with collective (fragment) moves, square-root sampling.
  • Ligand-Guided modeling of large dynamic proteins to predict alternative structural and functional states.
  • The Pocketome definition and derivation of all small molecule binding pockets with receptor flexibility and multiple ligands for target profiling and pharmacology prediction of leads and drugs.
  • Structure-based discovery of drug candidates with multi-target properties or with improved profiles in oncology, neurodegenerative diseases, viral, and parasitic infectious diseases. Several leads in clinical trials.